# HG changeset patch
# User elixir-it
# Date 1541761592 18000
# Node ID eaac11a49bd23e95469b67c6511217d66a9d9f82
Uploaded
diff -r 000000000000 -r eaac11a49bd2 bed_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_macros.xml Fri Nov 09 06:06:32 2018 -0500
@@ -0,0 +1,22 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r eaac11a49bd2 covacs_varscan2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_varscan2.xml Fri Nov 09 06:06:32 2018 -0500
@@ -0,0 +1,167 @@
+
+ varscan2 wrapper for covacs
+
+ varscan
+
+
+ bed_macros.xml
+
+
+
+
+
+
+ &1 | head -n 1
+ ]]>
+
+ samples_list.txt &&
+ #end if
+
+ ## Set up command + input.
+ varscan ${cmd} ${input}
+ --min-coverage ${min_coverage}
+ --min-reads2 ${min_supporting_reads}
+ --min-avg-qual ${min_avg_qual}
+ --min-var-freq ${min_var_freq}
+ --min-freq-for-hom ${min_freq_for_hom}
+ --p-value ${p_value}
+ #if str($strand_filter) == 'yes':
+ --strand-filter 1
+ #end if
+
+ ## Report only variants in consensus.
+ #if str($cmd) == 'mpileup2cns':
+ --variants
+ #end if
+
+ ## varscan bed limit added
+
+ #if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
+ limit $bed_source.bed_history
+ #end if
+ #if $bed_source.bed_source_selector == "cached"
+ limit $bed_source.bed_cached.fields.path
+ #end if
+
+ ## Set up outputs.
+ --output-vcf 1 > $output
+
+ #if $sample_names.strip() != '':
+ --vcf-sample-list samples_list.txt
+ #end if
+
+ && perl $__tool_directory__/filter.varscan.pl $output $output_filtered
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**VarScan Overview**
+
+VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1 Full documentation is available online_.
+
+.. _VarScan: http://dkoboldt.github.io/varscan/
+.. _online: http://dkoboldt.github.io/varscan/using-varscan.html
+
+**Input**
+
+::
+
+ mpileup file - The SAMtools mpileup file
+
+**the wrapper gives 2 output**
+
+-the normal output of varscan2
+
+-the output filtered by the filter.varscan.pl script implemented in the covacs pipeline
+
+
+
+**Parameters**
+
+::
+
+ analysis type
+ single nucleotide detection Identify SNPs from an mpileup file
+ insertions and deletion Identify indels an mpileup file
+ consensus genotype Call consensus and variants from an mpileup file
+
+ min-coverage
+ Minimum read depth at a position to make a call [8]
+
+ min-reads2
+ Minimum supporting reads at a position to call variants [2]
+
+ min-avg-qual
+ Minimum base quality at a position to count a read [15]
+
+ min-var-freq
+ Minimum variant allele frequency threshold [0.01]
+
+ min-freq-for-hom
+ Minimum frequency to call homozygote [0.75]
+
+ p-value
+ Default p-value threshold for calling variants [99e-02]
+
+ strand-filter
+ Ignore variants with >90% support on one strand [1]
+
+ output-vcf
+ If set to 1, outputs in VCF format
+
+ vcf-sample-list
+ For VCF output, a list of sample names in order, one per line
+
+ variants
+ Report only variant (SNP/indel) positions [0]
+
+
+
+ 10.1101/gr.129684.111
+ 10.1186/s12864-018-4508-1
+
+
diff -r 000000000000 -r eaac11a49bd2 filter.varscan.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.varscan.pl Fri Nov 09 06:06:32 2018 -0500
@@ -0,0 +1,22 @@
+#!/usr/bin/perl -w
+$f=shift;
+$outfile=shift;
+open(OUT,">$outfile");
+open(IN,$f);
+$head=;
+print OUT $head;
+while()
+{
+ if ($_=~/^\#/)
+ {
+ print OUT;
+ next;
+ }
+ $v=(split())[-1];
+ @vl=(split(/\:/,$v));
+ $vt=$vl[2];
+ if ($vt>=10)
+ {
+ print OUT;
+ }
+}
diff -r 000000000000 -r eaac11a49bd2 tool-data/covacs_bed.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/covacs_bed.loc.sample Fri Nov 09 06:06:32 2018 -0500
@@ -0,0 +1,17 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory bed file for covacs sequences data files. You will need
+#to create these data files and then create a bed_loc.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bed_loc.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
+hg19 hg19 hg19-padded /export/BED/S07084713_Padded.bed
+hgbed hg19 hg19-bed-test /export/BED/chr22.bed
diff -r 000000000000 -r eaac11a49bd2 tool-data/covacs_gatk_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/covacs_gatk_indexes.loc.sample Fri Nov 09 06:06:32 2018 -0500
@@ -0,0 +1,36 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of all covacs wrapper that need a gatk reference. You will need
+#to create these data files and then create a covacs_gatk_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The covacs_gatk_indexes.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had phiX indexed stored in
+#/depot/data2/galaxy/phiX/base/,
+#then the bwa_index.loc entry would look like this:
+#
+#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.dict, phiX.fa.fai files.
+#
+#
+#Your covacs_gatk_indexes.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
+hg38 hg38 hg38_GDC /export/gatkhg38pl/GRCh38.d1.vd1.fa
+hg19 hg19 hg19 /export/gatk_hg19_index_bundle/ucsc.hg19.fasta
diff -r 000000000000 -r eaac11a49bd2 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Nov 09 06:06:32 2018 -0500
@@ -0,0 +1,12 @@
+
+
+